Ferredoxin domain structure

Muller, J., Lugovskoy, A. A., Wagner, G., and Lippard, S.J. (2002) NMR structure of the [2Fe-2S] ferredoxin domain from soluble methane monooxygenase reductase and interaction with its hydroxylase. Biochemistry 41, 42-51. 

Fig. 10. The structure ofZJ. gigas Eildehyde oxidoreductase (AOR) monomer, showing the Mo-MCD site, the two [2Fe-2S] centers, and the tracing of the pol3ipeptide chain. The Fe-S center most exposed is included in a protein domain whose folding is quite similar to the one found in plant-type ferredoxins (199).

Figure 13.24 Structures of sMMO components and proposed reaction cycle, (a) MMOH (b) the MMOR FAD and ferredoxin (Fd) domains (c) MMOB. In MMOH the ot, P and y subunits are coloured blue, green and purple, respectively. Iron, sulfur and FAD are coloured orange, yellow and red, respectively and are depicted as spheres. The MMO reaction cycle is shown on the right, with atoms coloured [Fe (black), C (grey), O (red) and N (blue)]. (Reprinted with permission from Sazinsky and Lippard, 2006. Copyright (2006) American Chemical Society.)...

Fig. 105. Examples of small disulfide-rich or metal-rich proteins (shown on the right side) compared with their more regular counterparts in other structural categories (shown at the left), (a) Tobacco mosaic virus protein, an up-and-down helix bundle (b) cytochrome bs, a distorted up-and-down helix bundle (c) trypsin domain 1, a Greek key antiparallel /3 barrel (d) high-potential iron protein, a distorted Greek key /3 barrel (e) glutathione reductase domain 3, an open-face sandwich fi sheet (f) ferredoxin, a distorted open-face sandwich f) sheet.

Two [Fe] hydrogenase structures have so far been determined from C. pasteurianum (Cp) (Peters et al. 1998) and D. desulfuricans (Dd) (Nicolet et al. 1999). They have in common a large domain, which contains the catalytic site and three [4Fe-4S] iron sulfur clusters. The catalytic site and the closest (proximal) cluster are deeply buried inside the protein between two domains (or lobes), with access to a third, ferredoxin-like, domain that contains the two remaining (medial and distal) clusters. By contrast with [NiFe] hydrogenases the proximal [4Fe-4S] cluster is directly bridged to the bin-uclear active site by a cysteic thiolate (Fig. 6.12). 

Ferredoxins (Fds) are widespread in the three domains of life and an abundance of sequence data and structural information are available for Fds isolated from several sources. In particular, the bacterial type Fds are small electron-transfer proteins that posses cubane xFe-yS clusters attached to the protein matrix by Fe ligation of Cys via a conserved consensus ligating sequence. The archaeal type ferredoxins are water-soluble electron acceptors for the acyl-coenzyme A forming 2-oxoacid/ferredoxin oxidoreductase, a key enzyme involved in the central archaeal metabolic pathways. Fds have been distinguished according to the number of iron and inorganic sulphur atoms, 2Fe-2S, 4Fe-4S/3Fe-4S (Fig. Ib-d) and Zn-containing Fds. 

Figure 16-31 (A) Structure of molybdopterin cytosine dinucleotide complexed with an atom of molybdenum. (B) Stereoscopic ribbon drawing of the structure of one subunit of the xanthine oxidase-related aldehyde oxidoreductase from Desulfo-vibrio gigas. Each 907-residue subunit of the homodimeric protein contains two Fe2S2 clusters visible at the top and the molybdenum-molybdopterin coenzyme buried in the center. (C) Alpha-carbon plot of portions of the protein surrounding the molybdenum-molybdopterin cytosine dinucleotide and (at the top) the two plant-ferredoxin-like Fe2S2 clusters. Each of these is held by a separate structural domain of the protein. Two additional domains bind the molybdopterin coenzyme and there is also an intermediate connecting domain. In xanthine oxidase the latter presumably has the FAD binding site which is lacking in the D. gigas enzyme. From Romao et al.633 Courtesy of R. Huber.

The basic topology of the TRADD-N domain resembles the family of ferredoxin-like a-j3 sandwiches (Orengo and Thornton, 1993), which are often present as domains in larger structures such as the palm domain of... 

There are five classes of flavin-binding structural folds presented in Table 1 that are identified by the prototype protein in which they were first discovered. These are flavodoxin (FDX), ferredoxin reductase (FNR), triosephosphate isomerase (TIM), glutathione reductase (GR) and p-cresol methylhydroxylase (PCMH). The topologies of four of these five domains are shown in Figure 2. There are also four classes of primary acceptor/donor domain folds that are identified by the prototype protein where they were first discovered. They are cytochrome P450BMP (BMP), cytochrome b5 (CYTB5), cytochrome c (CYTC) and the 2Fe-2S plant-type ferredoxin (FDN). 

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